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Aliases for AGBL4 Gene

Aliases for AGBL4 Gene

  • ATP/GTP Binding Protein Like 4 2 3 5
  • Cytosolic Carboxypeptidase 6 2 3
  • CCP6 3 4
  • ATP/GTP-Binding Protein-Like 4 4
  • EC 3.4.17.- 4

External Ids for AGBL4 Gene

Previous GeneCards Identifiers for AGBL4 Gene

  • GC01M048762
  • GC01M048825
  • GC01M048998
  • GC01M047116

Summaries for AGBL4 Gene

GeneCards Summary for AGBL4 Gene

AGBL4 (ATP/GTP Binding Protein Like 4) is a Protein Coding gene. Diseases associated with AGBL4 include Macular Degeneration, Age-Related, 1. GO annotations related to this gene include tubulin binding and metallocarboxypeptidase activity. An important paralog of this gene is AGBL5.

UniProtKB/Swiss-Prot for AGBL4 Gene

  • Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes polyglutamates from the carboxy-terminus of target proteins such as MYLK. Mediates deglutamylation of CGAS/MB21D1, regulating the antiviral activity of CGAS/MB21D1. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5.

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for AGBL4 Gene

Genomics for AGBL4 Gene

Regulatory Elements for AGBL4 Gene

Enhancers for AGBL4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G049102 0.4 ENCODE 10.5 +921.0 921013 1.4 JUND JUNB LOC105378706 AGBL4 GC01M049179
GH01G049162 0.4 ENCODE 10.1 +860.8 860770 1.4 JUND SMARCA4 LOC105378706 AGBL4 GC01M049179
GH01G050023 0.7 ENCODE 0.7 +0.0 31 0.2 MAZ MXI1 RFX1 L3MBTL2 ZNF76 E2F1 ZFHX2 BCL11A RFX3 ZBTB48 AGBL4 MTND2P29
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around AGBL4 on UCSC Golden Path with GeneCards custom track

Promoters for AGBL4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000006195 -46 800 MAZ MXI1 RFX1 L3MBTL2 ZNF76 E2F1 ZFHX2 BCL11A RFX3 ZBTB48

Genomic Location for AGBL4 Gene

Chromosome:
1
Start:
48,532,834 bp from pter
End:
50,023,954 bp from pter
Size:
1,491,121 bases
Orientation:
Minus strand

Genomic View for AGBL4 Gene

Genes around AGBL4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
AGBL4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for AGBL4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for AGBL4 Gene

Proteins for AGBL4 Gene

  • Protein details for AGBL4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VU57-CBPC6_HUMAN
    Recommended name:
    Cytosolic carboxypeptidase 6
    Protein Accession:
    Q5VU57
    Secondary Accessions:
    • B3KT26
    • B4DG37

    Protein attributes for AGBL4 Gene

    Size:
    503 amino acids
    Molecular mass:
    58230 Da
    Cofactor:
    Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
    Quaternary structure:
    • Interacts with MYLK.
    SequenceCaution:
    • Sequence=BAG52938.1; Type=Frameshift; Positions=501; Evidence={ECO:0000305}; Sequence=BAG57648.1; Type=Frameshift; Positions=501; Evidence={ECO:0000305};

    Alternative splice isoforms for AGBL4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for AGBL4 Gene

Post-translational modifications for AGBL4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for AGBL4 Gene

Domains & Families for AGBL4 Gene

Gene Families for AGBL4 Gene

Protein Domains for AGBL4 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q5VU57

UniProtKB/Swiss-Prot:

CBPC6_HUMAN :
  • Belongs to the peptidase M14 family.
Family:
  • Belongs to the peptidase M14 family.
genes like me logo Genes that share domains with AGBL4: view

Function for AGBL4 Gene

Molecular function for AGBL4 Gene

UniProtKB/Swiss-Prot Function:
Metallocarboxypeptidase that mediates deglutamylation of target proteins. Catalyzes the deglutamylation of polyglutamate side chains generated by post-translational polyglutamylation in proteins such as tubulins. Also removes polyglutamates from the carboxy-terminus of target proteins such as MYLK. Mediates deglutamylation of CGAS/MB21D1, regulating the antiviral activity of CGAS/MB21D1. Acts as a long-chain deglutamylase and specifically shortens long polyglutamate chains, while it is not able to remove the branching point glutamate, a process catalyzed by AGBL5/CCP5.

Enzyme Numbers (IUBMB) for AGBL4 Gene

Gene Ontology (GO) - Molecular Function for AGBL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004181 metallocarboxypeptidase activity IEA,ISS --
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
GO:0008270 zinc ion binding IEA --
GO:0015631 tubulin binding ISS,IEA --
genes like me logo Genes that share ontologies with AGBL4: view
genes like me logo Genes that share phenotypes with AGBL4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for AGBL4 Gene

Localization for AGBL4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for AGBL4 Gene

Cytoplasm, cytosol. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole. Golgi apparatus. Cytoplasm, cytoskeleton, cilium basal body. Note=Colocalizes with gamma-tubulin in the centrioles at interphase and dividing cells and with glutamylated tubulin in basal bodies of ciliated cells. {ECO:0000269 PubMed:23085998}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for AGBL4 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
golgi apparatus 5
nucleus 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for AGBL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus IEA,IDA 23085998
GO:0005814 centriole IEA,IDA 23085998
GO:0005829 cytosol ISS --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with AGBL4: view

Pathways & Interactions for AGBL4 Gene

SuperPathways for AGBL4 Gene

No Data Available

Interacting Proteins for AGBL4 Gene

Gene Ontology (GO) - Biological Process for AGBL4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0035608 protein deglutamylation ISS,IEA --
GO:0035609 C-terminal protein deglutamylation ISS,IEA --
GO:0035610 protein side chain deglutamylation IEA,ISS --
GO:0051607 defense response to virus IEA,ISS --
genes like me logo Genes that share ontologies with AGBL4: view

No data available for Pathways by source and SIGNOR curated interactions for AGBL4 Gene

Drugs & Compounds for AGBL4 Gene

(1) Drugs for AGBL4 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Rifampin Approved Pharma Agonist 348
genes like me logo Genes that share compounds with AGBL4: view

Transcripts for AGBL4 Gene

mRNA/cDNA for AGBL4 Gene

Unigene Clusters for AGBL4 Gene

ATP/GTP binding protein-like 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for AGBL4 Gene

No ASD Table

Relevant External Links for AGBL4 Gene

GeneLoc Exon Structure for
AGBL4
ECgene alternative splicing isoforms for
AGBL4

Expression for AGBL4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for AGBL4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for AGBL4 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x7.4), Brain - Cortex (x7.4), and Brain - Anterior cingulate cortex (BA24) (x6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for AGBL4 Gene



NURSA nuclear receptor signaling pathways regulating expression of AGBL4 Gene:

AGBL4

SOURCE GeneReport for Unigene cluster for AGBL4 Gene:

Hs.551844

Evidence on tissue expression from TISSUES for AGBL4 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with AGBL4: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for AGBL4 Gene

Orthologs for AGBL4 Gene

This gene was present in the common ancestor of animals.

Orthologs for AGBL4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia AGBL4 34
  • 99.73 (n)
dog
(Canis familiaris)
Mammalia AGBL4 34
  • 92.51 (n)
cow
(Bos Taurus)
Mammalia AGBL4 34 35
  • 91.43 (n)
mouse
(Mus musculus)
Mammalia Agbl4 34 16 35
  • 89 (n)
rat
(Rattus norvegicus)
Mammalia LOC100911395 34
  • 88.33 (n)
oppossum
(Monodelphis domestica)
Mammalia AGBL4 35
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia AGBL4 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves AGBL4 34
  • 77.35 (n)
lizard
(Anolis carolinensis)
Reptilia AGBL4 35
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia agbl4 34
  • 71.96 (n)
Str.8458 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.12263 34
zebrafish
(Danio rerio)
Actinopterygii agbl4 34 35
  • 74.07 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001814 34
  • 55.19 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31019 34 35
  • 53.19 (n)
worm
(Caenorhabditis elegans)
Secernentea ccpp-6 34 35
  • 50.98 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 62 (a)
OneToOne
Species where no ortholog for AGBL4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for AGBL4 Gene

ENSEMBL:
Gene Tree for AGBL4 (if available)
TreeFam:
Gene Tree for AGBL4 (if available)

Paralogs for AGBL4 Gene

Paralogs for AGBL4 Gene

(4) SIMAP similar genes for AGBL4 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with AGBL4: view

Variants for AGBL4 Gene

Sequence variations from dbSNP and Humsavar for AGBL4 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs193921115 Uncertain significance 48,727,942(-) TGGAT(A/G)TCAAT intron-variant, nc-transcript-variant, reference, missense
rs1000001215 -- 49,970,500(+) ATCGG(G/T)GCCTG intron-variant
rs1000001254 -- 49,326,070(+) GTAGT(C/T)TGATA intron-variant
rs1000001606 -- 49,970,943(+) TTTAA(A/C)GCAGG intron-variant
rs1000002072 -- 49,838,824(+) CATTC(C/T)AGTGG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for AGBL4 Gene

Variant ID Type Subtype PubMed ID
dgv161n100 CNV loss 25217958
dgv162n100 CNV loss 25217958
dgv163n100 CNV loss 25217958
dgv164n100 CNV loss 25217958
dgv265n54 CNV loss 21841781
dgv266n54 CNV loss 21841781
dgv267n54 CNV loss 21841781
dgv33e212 CNV loss 25503493
dgv34e212 CNV loss 25503493
dgv81n106 CNV deletion 24896259
esv1114612 CNV deletion 17803354
esv1301667 CNV insertion 17803354
esv1541386 CNV deletion 17803354
esv22537 CNV gain 19812545
esv22622 CNV loss 19812545
esv2659799 CNV deletion 23128226
esv2662284 CNV deletion 23128226
esv2664027 CNV deletion 23128226
esv2668420 CNV deletion 23128226
esv2670528 CNV deletion 23128226
esv2674873 CNV deletion 23128226
esv2675645 CNV deletion 23128226
esv2677980 CNV deletion 23128226
esv2760076 CNV loss 21179565
esv2763301 CNV loss 21179565
esv2764215 CNV loss 21179565
esv28920 CNV loss 19812545
esv3302647 CNV tandem duplication 20981092
esv3303981 CNV mobile element insertion 20981092
esv3305785 CNV mobile element insertion 20981092
esv3306252 CNV mobile element insertion 20981092
esv3308453 CNV mobile element insertion 20981092
esv3309945 CNV mobile element insertion 20981092
esv3338226 CNV insertion 20981092
esv3344523 CNV insertion 20981092
esv3351275 CNV insertion 20981092
esv3370544 CNV insertion 20981092
esv3381286 CNV insertion 20981092
esv3396013 CNV insertion 20981092
esv3399424 CNV duplication 20981092
esv3407441 CNV insertion 20981092
esv3429396 CNV insertion 20981092
esv3561793 CNV deletion 23714750
esv3561826 CNV deletion 23714750
esv3561837 CNV deletion 23714750
esv3577841 CNV loss 25503493
esv3577842 CNV loss 25503493
esv3577843 CNV loss 25503493
esv3577845 CNV loss 25503493
esv3585970 CNV loss 21293372
esv3585973 CNV loss 21293372
esv3585974 CNV loss 21293372
esv3585976 CNV loss 21293372
esv3585978 CNV loss 21293372
esv3585984 CNV loss 21293372
esv3585985 CNV loss 21293372
esv3585986 CNV loss 21293372
esv3585987 CNV loss 21293372
esv3585988 CNV loss 21293372
esv3585989 CNV loss 21293372
esv3585990 CNV loss 21293372
esv3585992 CNV loss 21293372
esv3585993 CNV loss 21293372
esv3585995 CNV loss 21293372
esv3585997 CNV loss 21293372
esv3585998 CNV loss 21293372
esv3585999 CNV loss 21293372
esv3586002 CNV loss 21293372
esv3586003 CNV loss 21293372
esv3586004 CNV loss 21293372
esv3893534 CNV loss 25118596
esv3893546 CNV loss 25118596
esv992229 CNV insertion 20482838
nsv1003151 CNV loss 25217958
nsv1003968 CNV gain 25217958
nsv1006879 CNV loss 25217958
nsv1011119 CNV loss 25217958
nsv1011949 CNV loss 25217958
nsv1013711 CNV loss 25217958
nsv1014234 CNV loss 25217958
nsv1076421 CNV deletion 25765185
nsv1110130 CNV duplication 24896259
nsv1119686 CNV deletion 24896259
nsv1119687 CNV deletion 24896259
nsv1124568 CNV duplication 24896259
nsv1133849 CNV deletion 24896259
nsv1141894 OTHER inversion 24896259
nsv160710 CNV deletion 16902084
nsv475812 CNV novel sequence insertion 20440878
nsv476553 CNV novel sequence insertion 20440878
nsv477304 CNV novel sequence insertion 20440878
nsv509235 CNV insertion 20534489
nsv516709 CNV loss 19592680
nsv518328 CNV loss 19592680
nsv521306 CNV loss 19592680
nsv521615 CNV loss 19592680
nsv525248 CNV loss 19592680
nsv527526 CNV loss 19592680
nsv546193 CNV loss 21841781
nsv546194 CNV loss 21841781
nsv546195 CNV loss 21841781
nsv546196 CNV loss 21841781
nsv777 CNV insertion 18451855
nsv788 CNV insertion 18451855
nsv799 CNV insertion 18451855
nsv819895 CNV gain 19587683
nsv829771 CNV gain 17160897
nsv829782 CNV loss 17160897
nsv829793 CNV gain 17160897
nsv829804 CNV loss 17160897
nsv829815 CNV gain 17160897
nsv945934 CNV duplication 23825009
nsv998640 CNV loss 25217958

Variation tolerance for AGBL4 Gene

Gene Damage Index Score: 4.81; 66.99% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for AGBL4 Gene

Human Gene Mutation Database (HGMD)
AGBL4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
AGBL4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for AGBL4 Gene

Disorders for AGBL4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for AGBL4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
macular degeneration, age-related, 1
  • macular degeneration, age-related, reduced risk of
- elite association - COSMIC cancer census association via MalaCards
Search AGBL4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for AGBL4

Genetic Association Database (GAD)
AGBL4
Human Genome Epidemiology (HuGE) Navigator
AGBL4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
AGBL4
genes like me logo Genes that share disorders with AGBL4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for AGBL4 Gene

Publications for AGBL4 Gene

  1. Functional segregation and emerging role of cilia-related cytosolic carboxypeptidases (CCPs). (PMID: 23085998) Rodriguez de la Vega Otazo M. … Bautista J.M. (FASEB J. 2013) 3 4 64
  2. A family of protein-deglutamylating enzymes associated with neurodegeneration. (PMID: 21074048) Rogowski K. … Janke C. (Cell 2010) 2 3 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G. … Wijmenga C. (Gut 2009) 3 46 64
  5. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory S.G. … Bentley D.R. (Nature 2006) 3 4 64

Products for AGBL4 Gene

Sources for AGBL4 Gene

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